fastq --> SAM --> BAM --> VCF --> consensus_seq/snps
But if multiple samples are given (with snippy-multi option) it outputs an aligned fasta format. My understanding so far is it doesn't go through any MSA alignment algorithm, but use the pairwise alignment information from SAM files.
How is the aligned fasta file generated? The log file doesn't contain information about how snippy calculates it. Is there any other tool that I can use to get similar aligned fasta file from SAM/VCF file without going through any actual MSA algorithm?